PubMed

J Clin Endocrinol Metab. 2024 Nov 28:dgae737. doi: 10.1210/clinem/dgae737. Online ahead of print.ABSTRACTCONTEXT: Primary hypertrophic osteoarthropathy (PHO) is a rare genetic disorder characterized by skeletal and skin abnormalities. Genetic defects in prostaglandin E2 (PGE2) metabolism are known to cause PHO. However, the global impact and clinical significance of eicosanoids and oxylipins beyond PGE2 remain to be elucidated.OBJECTIVE: This study aimed to investigate oxylipin networks in PHO, including the 2 subtypes, PHOAR1 and PHOAR2, and examine their associations with clinical characteristics.METHODS: We conducted a targeted metabolomic study involving 16 patients with PHO and 16 age- and sex-matched healthy controls. Serum samples were collected at the time of diagnosis. Metabolites were quantified using ultra-high-performance liquid chromatography-tandem mass spectrometry.RESULTS: Laboratory analyses confirmed elevated levels of PGE2 in patients with PHO, consistent with the established pathogenesis. About 60 oxidized lipid metabolites were identified, with 19 differentially expressed in PHO. Besides the COX/PGE2 pathway, the lipoxygenase-mediated pathway was also involved in PHO. The metabolites 5-OxoETE, 15-OxoETE, 8S,15S-DiHETE, PGE2, 11β-PGE2, PGB2, LTB4, and LTE4 were significantly altered. Correlation analyses revealed associations between oxylipin metabolites and clinical features, including bone microarchitecture. Notably, the study highlighted differences in the oxylipin metabolite profiles between patients with PHOAR1 and patients with PHOAR2, suggesting distinct metabolic signatures for each subtype.CONCLUSION: Our study indicated a significant perturbation in oxylipin metabolism among patients with PHO, with distinct metabolic signatures observed between PHOAR1 and PHOAR2. The disruption extended beyond the metabolism of PGE2. It encompassed a broader alteration across the polyunsaturated fatty acid metabolism spectrum, including various eicosanoids and oxylipins. Our work provided a comprehensive understanding of the pathogenesis of PHO, and underscored the potential for subtype-specific therapeutic interventions.PMID:39607761 | DOI:10.1210/clinem/dgae737

J Gerontol A Biol Sci Med Sci. 2024 Nov 28:glae272. doi: 10.1093/gerona/glae272. Online ahead of print.ABSTRACTSkin autofluorescence (SAF), reflecting advanced glycation end-products' accumulation in tissue, has been proposed as a non-invasive aging biomarker. Yet, SAF has not been compared to well-established blood-based aging biomarkers such as MetaboHealth in association with frailty. Furthermore, no previous study determined the longitudinal association of SAF with frailty. We used 2382 Doetinchem Cohort Study participants' (aged 46.0 to 85.4) cross-sectional data, of whom 1654 had longitudinal SAF measurements. SAF was measured using the AGE reader™. MetaboHealth was calculated on 1H-NMR-metabolomics. Linear regressions were used for the associations of SAF and MetaboHealth on the 36-deficit frailty index and logistic regressions for being pre-frail or frail as determined by the frailty phenotype. Longitudinal associations were determined by an interaction term between age and SAF in a linear mixed model. SAF and MetaboHealth were associated with higher odds of pre-frailty (odd ratios per standard deviation SAF: 1.21(1.10;1.32), MetaboHealth: 1.35(1.24;1.49)) and frailty (SAF: 1.70(1.41;2.06), MetaboHealth: 1.90(1.57;2.32)). When mutually adjusted, both aging biomarkers remained associated with pre-frailty (SAF: 1.16(1.05;1.27), MetaboHealth 1.33(1.21;1.46)) and frailty (SAF: 1.52(1.25;1.85), MetaboHealth: 1.75(1.43;2.14)). Additionally, SAF and MetaboHealth were associated with higher frailty index scores (percentage increase per standard deviation SAF:1.35(1.00;1.70), MetaboHealth: 1.87(1.54;2.20)), also after mutual adjustment (SAF: 1.02(0.68;1.37), MetaboHealth: 1.69(1.35;2.02)). SAF was also longitudinally associated with the frailty index (percentage per unit/year increase 0.12(0.07;0.16)). The mutual independence of SAF and MetaboHealth implies they capture distinct aspects of the aging process. Altogether, these findings emphasize SAF's clinical potential as an age-related decline biomarker, which could be further enhanced when combined with MetaboHealth.PMID:39607723 | DOI:10.1093/gerona/glae272

Metab Brain Dis. 2024 Nov 28;40(1):45. doi: 10.1007/s11011-024-01450-4.ABSTRACTRadix Bupleuri-Radix Paeoniae Alba herb pair (RB-RPA) is the fundamental medication combination of many classic antidepressant prescriptions, and RB-RPA's antidepressant effect is well established. For an extended period, the involvement of intestinal flora in the progression of depression has been widely acknowledged. However, it remains unclear whether RB-RPA could modulate intestinal microbiota disturbances and metabolic abnormalities induced by depression. The research explores the antidepressant mechanism of RB-RPA in chronic unpredictable mild stress (CUMS) rats in terms of intestinal flora and metabolites. We identified critical gut microbial species and metabolites associated with the antidepressant effects of RB-RPA using 16 S rRNA sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics. And then, correlation analysis between critical microbiota and differential metabolites was conducted. The results demonstrate that RB-RPA significantly ameliorated depressive-like behavior in CUMS rats. RB-RPA improved intestinal flora disorders in depressed rats mainly by increasing the abundance of Lactobacillus (especially L. johnsonii), and ameliorated tryptophan synthesis and metabolism disorders in depressed rats and restored the levels of tryptophan and tryptophan microbial metabolites, such as indoleacrylic acid and 4-indoleacetaldehyde. Notably, correlation analysis showed that Lactobacillus had a significant positive correlation with tryptophan, indoleacrylic acid, and 4-indoleacetaldehyde. In conclusion, RB-RPA can improve the disorder of intestinal flora by increasing the abundance of Lactobacillus and improve the metabolic disorder of depressed rats by regulating tryptophan metabolism, thus exerting antidepressant effects.PMID:39607539 | DOI:10.1007/s11011-024-01450-4

Chempluschem. 2024 Nov 28:e202400605. doi: 10.1002/cplu.202400605. Online ahead of print.ABSTRACTZr-monosubstituted polyoxometalates (Zr-POMs) of the Keggin (Bu4N)8[{PW11O39Zr(μ-OH)}2] (Zr-K), Lindqvist (Bu4N)6[{W5O18Zr(μ-OH)}2] (Zr-L), and Wells-Dawson (Bu4N)11H3[{P2W17O61Zr(μ-OH)}2] (Zr-WD) structures are capable of heterolytic activation of the environmentally benign oxidant tert-butyl hydroperoxide (TBHP) and catalyze epoxidation of alkenes and oxidation of alcohols to carbonyl compounds. Catalytic activity of corresponding Ti-POMs is much lower. Among Zr-POMs, Zr-K revealed higher epoxide yields. All Zr-POMs do not catalyze unproductive TBHP degradation, and epoxide yields with both aqueous and anhydrous TBHP are generally higher than with aqueous H2O2. Regioselectivity of the Zr-K-catalyzed limonene epoxidation with TBHP is different from that with H2O2: the more substituted and nucleophilic double bond is preferably epoxidized, pointing to an electrophilic oxygen transfer mechanism. The oxidation rates are first order in catalyst (Zr-K) and substrate (cyclooctene or cyclohexanol) and show a saturation behavior with increasing concentration of TBHP. Studies by HR-ESI-MS, ATR-FT-IR, and 31P NMR spectroscopic techniques implicated the formation of zirconium alkylperoxo species upon interaction of Zr-POMs with TBHP. HR-ESI-MS revealed the existence of monomeric and dimeric alkylperoxo complexes, [{PW11O39Zr}((CH3)3COO)]4- and [{PW11O39Zr((CH3)3COO)}2]8-, with predomination of the former, which is most likely the active species responsible for the selective oxidations.PMID:39606905 | DOI:10.1002/cplu.202400605

J Dev Orig Health Dis. 2024 Nov 28;15:e30. doi: 10.1017/S2040174424000345.ABSTRACTNutrition is the critical nongenetic factor that has a major influence on the health status of an organism. The nutritional status of the mother during gestation and lactation plays a vital role in defining the offspring's health. Undernutrition during these critical periods may induce chronic metabolic disorders like obesity and cardiovascular diseases in mothers as well as in offspring. The present study aims to evaluate the impact of undernutrition during gestational and lactational periods on the plasma metabolic profile of dams. Additionally, we investigated the potential synergistic mitigating effects of astaxanthin and docosahexaenoic acid (DHA) on dysregulated plasma metabolic profiles. Evaluation of plasma lipid profile revealed that undernourishment resulted in elevated levels of total cholesterol, triglycerides, low density and very low-density lipoproteins in dams. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based untargeted metabolomics illustrated that pathways related to lipid metabolism, such as cholesterol metabolism, steroid biosynthesis and metabolism of amine-derived hormones, were dysregulated by undernourishment. Additionally, pathway enrichment analysis predicted that there is a high incidence of development of desmosterolosis, hypercholesterolaemia, lysosomal acid lipase deficiency and Smith-Lemli-Opitz syndrome in the offspring, reflecting predisposition in mothers. However, synergistic supplementation of astaxanthin and DHA ameliorated these adverse effects by regulating a separate set of metabolic pathways associated with lipid metabolism. They included branched chain amino acid degradation such as valine, leucine and isoleucine, metabolism of alpha-linolenic acid, lipoic acid, lysine degradation, biosynthesis, elongation and degradation of fatty acids.PMID:39606856 | DOI:10.1017/S2040174424000345

ArXiv [Preprint]. 2024 Nov 25:arXiv:2411.14464v2.ABSTRACTMOTIVATION: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP), annotation rates remain low.RESULTS: We introduce in this paper a novel paradigm (JESTR) for annotation. Unlike prior approaches that explicitly construct molecular fingerprints or spectra, JESTR leverages the insight that molecules and their corresponding spectra are views of the same data and effectively embeds their representations in a joint space. Candidate structures are ranked based on cosine similarity between the embeddings of query spectrum and each candidate. We evaluate JESTR against mol-to-spec and spec-to-FP annotation tools on three datasets. On average, for rank@[1-5], JESTR outperforms other tools by 23.6%-71.6%. We further demonstrate the strong value of regularization with candidate molecules during training, boosting rank@1 performance by 11.4% and enhancing the model's ability to discern between target and candidate molecules. Through JESTR, we offer a novel promising avenue towards accurate annotation, therefore unlocking valuable insights into the metabolome.PMID:39606728 | PMC:PMC11601792

Front Vet Sci. 2024 Nov 13;11:1475397. doi: 10.3389/fvets.2024.1475397. eCollection 2024.ABSTRACTMastitis is a disease with frequent incidence in dairy cows, causing huge financial losses to the dairy industry globally. The identification of certain biomarkers is crucial for the early diagnosis and management of mastitis. Metabolomics technology is a useful tool to accurately and efficiently analyze the changes of metabolites in biofluids in response to internal and external stimulations. Milk is the secreted by udder, and milk metabolites can directly reflect whether the udder are in the healthy or diseased state. The milk metabolomics analysis of mastitis can reveal the physiological and pathological changes of mammary gland and screen the related biomarkers, so as to offer useful reference for the prediction, diagnosis, and management of mastitis. Therefore, the aim of the present study was to comprehensively summarize milk metabolic change caused by naturally occurring or experimentally induced mastitis in dairy cows. In addition, comparative analysis and enrichment analysis were conducted to further discover potential biomarkers of mastitis and to identify the relevant pathways differentiating the healthy and mastitic cows. Multiple milk metabolites were identified to be altered during mastitis based on different metabolomics platforms. It was noteworthy that there were 28 metabolites not only identified by at least two different studies, but also showed consistent change tendency among the different studies. By comparison with literature, we further identified 12 milk metabolites, including acetate, arginine, β-hydroxybutyrate, carnitine, citrate, isoleucine, lactate, leucine, phenylalanine, proline, riboflavin, and valine that were linked with the occurrence of mastitis, which suggested that these 12 milk metabolites could be potential biomarkers of mastitis in dairy cows. Several pathways were revealed to explain the mechanisms of the variation of milk metabolites caused by mastitis, such as phenylalanine, tyrosine and tryptophan biosynthesis, arginine and proline metabolism, riboflavin metabolism, and tricarboxylic acid (TCA) cycle. These results offer a further understanding for the alteration of milk metabolites caused by mastitis, which have a potential significance in the development of more reliable biomarkers for mastitic diagnosis in dairy cows.PMID:39606657 | PMC:PMC11598933 | DOI:10.3389/fvets.2024.1475397

Res Sq [Preprint]. 2024 Nov 12:rs.3.rs-5391023. doi: 10.21203/rs.3.rs-5391023/v1.ABSTRACTAntibiotic resistance is one of the most pressing threats to human health, yet recent work highlights how loss of resistance may also drive pathogenesis in some bacteria. In two recent studies, we found that β-lactam antibiotic and nutrient stresses faced during infection selected for the genetic inactivation of the Pseudomonas aeruginosa (Pa) antibiotic efflux pump mexEFoprN. Unexpectedly, efflux pump mutations increased Pa virulence during infection; however, neither the prevalence of efflux pump inactivating mutations in real human infections, nor the mechanisms driving increased virulence of efflux pump mutants are known. We hypothesized that human infection would select for efflux pump mutations that drive increased virulence in Pa clinical isolates. Using genome sequencing of hundreds of Pa clinical isolates, we show that mexEFoprN efflux pump inactivating mutations are enriched in Pa cystic fibrosis isolates relative to Pa intensive care unit clinical isolates. Combining RNA-seq, metabolomics, genetic approaches, and infection models we show that efflux pump mutants have elevated expression of two key Pa virulence factors, elastase and rhamnolipids, which increased Pa virulence and lung damage during both acute and chronic infections. Increased virulence factor production was driven by higher Pseudomonas quinolone signal levels in the efflux pump mutants. Finally, genetic restoration of the efflux pump in a representative ICU clinical isolate and the notorious CF Pa Liverpool epidemic strain reduced their virulence. Together, our findings suggest that mutations inactivating antibiotic resistance mechanisms could lead to greater patient mortality and morbidity.PMID:39606469 | PMC:PMC11601840 | DOI:10.21203/rs.3.rs-5391023/v1

Metabolomics. 2017 May;13(5):50. doi: 10.1007/s11306-017-1188-9. Epub 2017 Mar 6.ABSTRACTINTRODUCTION: The Metabolomics Society Data Quality Task Group (DQTG) developed a questionnaire regarding quality assurance (QA) and quality control (QC) to provide baseline information about current QA and QC practices applied in the international metabolomics community.OBJECTIVES: The DQTG has a long-term goal of promoting robust QA and QC in the metabolomics community through increased awareness via communication, outreach and education, and through the promotion of best working practices. An assessment of current QA and QC practices will serve as a foundation for future activities and development of appropriate guidelines.METHOD: QA was defined as the set of procedures that are performed in advance of analysis of samples and that are used to improve data quality. QC was defined as the set of activities that a laboratory does during or immediately after analysis that are applied to demonstrate the quality of project data. A questionnaire was developed that included 70 questions covering demographic information, QA approaches and QC approaches and allowed all respondents to answer a subset or all of the questions.RESULT: The DQTG questionnaire received 97 individual responses from 84 institutions in all fields of metabolomics covering NMR, LC-MS, GC-MS, and other analytical technologies.CONCLUSION: There was a vast range of responses concerning the use of QA and QC approaches that indicated the limited availability of suitable training, lack of Standard Operating Procedures (SOPs) to review and make decisions on quality, and limited use of standard reference materials (SRMs) as QC materials. The DQTG QA/QC questionnaire has for the first time demonstrated that QA and QC usage is not uniform across metabolomics laboratories. Here we present recommendations on how to address the issues concerning QA and QC measurements and reporting in metabolomics.PMID:39606286 | PMC:PMC11601953 | DOI:10.1007/s11306-017-1188-9

Chin Herb Med. 2024 Mar 26;16(4):599-611. doi: 10.1016/j.chmed.2024.02.001. eCollection 2024 Oct.ABSTRACTOBJECTIVE: To investigate the mechanisms that underlie the anti-asthmatic effects of Nepeta bracteata (DBJJ, Dabao Jingjie in Chinese) in rats by integrating metabolomics and network pharmacology.METHODS: In this study, the rat model of asthma was induced by ovalbumin (OVA), and the rats were treated with a decoction of N. bracteata. Pathological changes in lung tissue were observed, and the quantification of eosinophils (EOS) and white blood cells (WBC) in bronchoalveolar lavage fluid was performed. Furthermore, the serum levels of asthma-related factors induced by OVA were assessed. 1H NMR spectroscopy serum metabolomics method was utilized to identify differential metabolites and their associated metabolic pathways. UPLC-QE-MS/MS combined with network pharmacology was employed to predict the core targets and pathways of DBJJ in its action against asthma. The anti-asthmatic properties of DBJJ were investigated using an integrated approach of metabolomics and network pharmacology. The findings were validated through molecular docking and Western blotting analysis of the key targets.RESULTS: The administration of DBJJ effectively alleviated OVA-induced lung histopathological changes and decreased the number of EOS and WBC in BALF. Additionally, DBJJ inhibited the OVA-induced elevation of TNF-α, IL-18, Ig-E, EOS, IL-1β, MDA, VEGF-A, and TGF-β1. A total of 21 biomarkers and 10 pathways were found by metabolomics analysis. A total of 29 compounds were identified by UPLC-QE-MS/MS, in which 13 active components were screened by oral availability and Caco-2 cell permeability, the 120 targets and 173 KEGG pathways were predicted. The integration of metabolomics and network pharmacological analysis revealed that DBJJ's main constituents, including ferulic acid and ursolic acid, exerted their effects on four targets, namely DAO and NOS2, as well as their associated metabolites and pathways. The active constituents of DBJJ demonstrated a high binding affinity towards DAO and NOS2. Furthermore, DBJJ was observed to decrease the protein expression and phosphorylation levels of NOS2, MAPK, and STAT3.CONCLUSION: The administration of DBJJ demonstrates notable anti-asthma properties in rats with allergic asthma. This effect can be attributed to the modulation of various targets, including NOS2, MAPK, and STAT3, by primary constituents such as ferulic acid and ursolic acid.PMID:39606263 | PMC:PMC11589474 | DOI:10.1016/j.chmed.2024.02.001

Chin Herb Med. 2024 Jul 29;16(4):638-655. doi: 10.1016/j.chmed.2024.07.007. eCollection 2024 Oct.ABSTRACTOBJECTIVE: Qingfei Tongluo Plaster (QFP), an improved Chinese medicine hospital preparation, is an attractive treatment option due to its well clinical efficacy, convenience, economy, and patient compliance in the treatment of respiratory syncytial virus (RSV) pneumonia. The aim of this study was to investigate the efficacy mechanism of QFP on RSV rats from the perspective of alleviating lung inflammation and further explore the changes of serum metabolites and metabolic pathways in RSV rats under the influence of QFP.METHODS: This study used network pharmacological methods and molecular docking combined with molecular biology and metabolomics from multi-dimensional perspectives to screen and verify the therapeutic targets. Open online databases were used to speculate the gene targets of efficient ingredients and diseases. Then, we used the String database to examine the fundamental interaction of common targets of drugs and diseases. An online enrichment analysis was performed to predict the functional pathways. Molecular docking was applied to discover the binding modes between essential ingredients and crucial gene targets. Finally, we demonstrated the anti-inflammatory ability of QFP in the RSV-evoked pneumonia rat model and explained the mechanism in combination with the metabolomics results.RESULTS: There were 19 critical targets defined as the core targets: tumor necrosis factor (TNF), inducible nitric oxide synthase 2 (NOS2), mitogen-activated protein kinase 14 (MAPK14), g1/S-specific cyclin-D1 (CCND1), signal transducer and activator of transcription 1-alpha/beta (STAT1), proto-oncogene tyrosine-protein kinase Src (SRC), cellular tumor antigen p53 (TP53), interleukin-6 (IL6), hypoxia-inducible factor 1-alpha (HIF1A), RAC-alpha serine/threonine-protein kinase (AKT1), signal transducer and activator of transcription 3 (STAT3), heat shock protein HSP 90-alpha (HSP90AA1), tyrosine-protein kinase JAK2 (JAK2), cyclin-dependent kinase inhibitor 1 (CDKN1A), mitogen-activated protein kinase 3 (MAPK3), epidermal growth factor receptor (EGFR), myc proto-oncogene protein (MYC), protein c-Fos (FOS) and transcription factor p65 (RELA). QFP treated RSV pneumonia mainly through the phosphatidylinositol 3-kinase (PI3K)/RAC AKT pathway, HIF-1 pathway, IL-17 pathway, TNF pathway, and MAPK pathway. Animal experiments proved that QFP could effectively ameliorate RSV-induced pulmonary inflammation. A total of 28 metabolites underwent significant changes in the QFP treatment, and there are four metabolic pathways consistent with the KEGG pathway analyzed by network pharmacology, suggesting that they may be critical processes related to treatment.CONCLUSION: These results provide essential perspicacity into the mechanisms of action of QFP as a promising anti-RSV drug.PMID:39606255 | PMC:PMC11589485 | DOI:10.1016/j.chmed.2024.07.007

Chin Herb Med. 2024 Aug 22;16(4):505-520. doi: 10.1016/j.chmed.2024.08.002. eCollection 2024 Oct.ABSTRACTPanax L. (Araliaceae) has a long history of medicinal and edible use due to its significant tonifying effects, and ginseng research has been a hot topic in natural products research and food science. In continuation of our recent ginseng review, we highlighted the advances in ginseng research from 2021 to 2023 with 157 citations, which exhibited the increasingly systematic, collaborative, and intelligent characteristics. In this review, we firstly updated the progress in phytochemistry involving the ginsenosides and polysaccharides and summarized the researches on the active components. Then, some specific applications by feat of the multidimensional chromatography, mass spectrometry imaging, DNA barcoding, and metabolomics, were analyzed, which could provide rich information supporting the multi-component characterization, authentication, and quality control of ginseng and the versatile products. Finally, the recent biosynthesis studies concerning ginsenosides were retrospected. Additionally, the current challenges and future trends with respect to ginseng research were discussed.PMID:39606254 | PMC:PMC11589329 | DOI:10.1016/j.chmed.2024.08.002

ACS Appl Polym Mater. 2024 Nov 6;6(22):13710-13722. doi: 10.1021/acsapm.4c02485. eCollection 2024 Nov 22.ABSTRACTPhysical cues have been shown to be effective in inducing osteogenic differentiation of mesenchymal stem cells (MSCs). Here, we propose piezoelectric stimulation as a potential osteogenic cue mimicking the electroactive properties of bone's extracellular matrix. When combined with a magnetostrictive component, piezoelectric polymers can be used for MSC stimulation by applying an external magnetic field. The deformation of the magnetostrictive component produces a deformation in the polymer matrix, generating a change in the surface charge that induces an electric field that can be transmitted to the cells. Cell adhesion, cytoskeleton changes, and metabolomics are the first evidence of MSC osteoblastogenesis and can be used to study initial MSC response to this kind of stimulation. In the current study, poly(vinylidene) fluoride (PVDF) piezoelectric films with and without cobalt ferrite oxide (CFO) crystallized from the melt in the presence of the ionic liquid 1-butyl-3-methyl-imidazolium chloride ([Bmim][Cl]) were produced. [Bmim][Cl] allowed the production of the β-phase, the most electroactive phase, even without CFO. After ionic liquid removal, PVDF and PVDF-CFO films presented high percentages of the β-phase and similar crystalline content. Incorporating CFO nanoparticles was effective, allowing the electromechanical stimulation of MSCs by applying a magnetic field with a bioreactor. Before stimulation, the initial response of MSCs was characterized in static conditions, showing that the produced films were biocompatible and noncytotoxic, allowing MSC adhesion and proliferation in the short term. Stimulation experiments revealed that MSCs electromechanically stimulated for 3 days in PVDF-CFO supports showed longer focal adhesions and decreased vimentin cytoskeletal density, both signals of early osteogenic differentiation. Furthermore, they rearranged their energy metabolism toward an osteogenic phenotype after 7 days of culture under the same stimulation. The results prove that MSCs respond to electromechanical stimulation by osteogenic differentiation.PMID:39606252 | PMC:PMC11590054 | DOI:10.1021/acsapm.4c02485

Front Immunol. 2024 Nov 13;15:1454334. doi: 10.3389/fimmu.2024.1454334. eCollection 2024.ABSTRACTThe gut-liver axis in ruminants can explain nutrient regulation, the gut-liver cycle, and immune function in ruminant biology through the gut microbe-gut metabolite-liver metabolite relationship. to investigate the effects of herbal feed additives on the gut-liver axis of Hu sheep. In this study, a broadly targeted UPLC-MS/MS metabolomics approach and 16s sequencing of gut microorganisms were used to detect, identify and quantify changes in ileal microorganisms, liver metabolites and ileal metabolites following the addition of Chinese herbal preparations. The addition of a 0.5% herbal feed additive increased ileal IgA, IgG and complement C3 levels. The addition of Chinese herbal preparations can increase the abundance of Firmicutes, Actinobacteriota, Bacteroidota, at the portal level of the ileum, increase the metabolism of organic matter and its derivatives, bile acids, amino acids and their metabolites, coenzymes, and vitamins in the liver and ileum, enhance nutrient absorption and waste metabolism, accelerate liver metabolism, promote gut-liver circulation, and improve ileal and liver immunity. This study provides a theoretical basis for understanding the effects of herbal feed additives on the gut-liver axis in ruminants.PMID:39606237 | PMC:PMC11599181 | DOI:10.3389/fimmu.2024.1454334

Front Pharmacol. 2024 Nov 13;15:1486739. doi: 10.3389/fphar.2024.1486739. eCollection 2024.ABSTRACTIt is well documented that immunosuppression in chickens increases the risk of secondary infections and immunodeficiencies, resulting in significant financial setbacks for the poultry sector. It is crucial to determine if Lycium barbarum polysaccharide (LBP) can counteract immune suppression in young chickens, considering its known ability to modulate immune responses. The aim of this study was to investigate the antagonistic effect and mechanism of LBP on immunosuppression in chicks. A total of 200 seven-day-old Hyland Brown laying hens were used to develop an immunosuppression model and to investigate the optimal time of use and optimal dosage of LBP. A further 120 seven-day-old Hyland Brown laying hens were used to investigate the mechanism of antagonism of LBP against immunosuppression at the optimal time and dosage. The results demonstrated that LBP significantly elevated body weight, spleen index, and peripheral lymphocyte transformation rate, and ameliorated pathological spleen damage in immunosuppressed chickens. A total of 178 differential genes were significantly upregulated following LBP intervention, with a significant enrichment in immune-related pathways, including the chemokine signalling pathway, the C-type lectin receptor signalling pathway, the B-cell receptor signalling pathway, platelet activation, natural killer cell-mediated cytotoxicity, and Th1 and Th2 cell differentiation. A total of 20 different metabolites were identified by metabolomics, which were mainly involved in vitamin metabolism, lipid metabolism, nucleic acid metabolism and amino acid metabolism. The integrated examination of transcriptomic and metabolomic data revealed that the glycerophospholipid metabolic pathway stands out as the most significant among all metabolic pathways. The results demonstrated that LBP regulate the immune system in a multi-pathway and multi-target way.PMID:39605922 | PMC:PMC11599638 | DOI:10.3389/fphar.2024.1486739

Front Pharmacol. 2024 Nov 13;15:1505231. doi: 10.3389/fphar.2024.1505231. eCollection 2024.ABSTRACTINTRODUCTION: The XuLing JianGu recipe (XLJGR) is an empirical traditional Chinese medicine formula used for the treatment of osteoporosis. This study aims to explore the effects of XLJGR on the intestinal microbiota composition and endogenous metabolites in ovariectomized (OVX) rats.METHODS: An OVX rat model was established to evaluate the intervention effects of XLJGR. The measured indicators included bone density, serum bone metabolism markers, and an analysis of the types and abundances of intestinal microbiota, along with changes in endogenous metabolites. Additionally, MC3T3-E1 cells were used to validate the differential metabolites.RESULTS: XLJGR significantly reduced the abundance of Bacteroides, Butyricicoccus, and other bacterial strains in the gut. KEGG metabolic pathway enrichment analysis showed that XLJGR intervention led to notable changes in pathways such as peptidoglycan biosynthesis, carbapenem biosynthesis, and vancomycin resistance. Moreover, XLJGR significantly upregulated key intestinal microbiota metabolites, including gabapentin(GAB), camphoric acid(CAA), and nonanedioic acid(AZA), thereby promoting the proliferation and osteogenic differentiation of MC3T3-E1 cells.DISCUSSION: This study highlights the potential biomedical applications of XLJGR in promoting bone health by positively affecting intestinal microbiota and metabolic characteristics. These findings suggest that XLJGR may serve as a viable alternative in the treatment of osteoporosis, warranting further exploration of its therapeutic mechanisms and clinical applications.PMID:39605913 | PMC:PMC11598424 | DOI:10.3389/fphar.2024.1505231

Front Physiol. 2024 Nov 13;15:1486767. doi: 10.3389/fphys.2024.1486767. eCollection 2024.ABSTRACTINTRODUCTION: Effects and interactions between different spaceflight stressors are expected to be experienced by crew on missions when exposed to microgravity and galactic cosmic rays (GCRs). One of the limitations of previous studies on simulated weightlessness using hindlimb unloading (HU) is that a control HU condition was not included.METHODS: We characterized the behavioral performance of male Fischer rats 2 months after sham or total body irradiation with a simplified 5-ion 6-mixed-beam exposure representative of GCRs in the absence or presence of HU. Six months later, the plasma, hippocampus, and cortex were processed to determine whether the behavioral effects were associated with long-term alterations in the metabolic pathways.RESULTS: In the open field without and with objects, interactions were observed for radiation × HU. In the plasma of animals that were not under the HU or control HU condition, the riboflavin metabolic pathway was affected most for sham irradiation vs. 0.75 Gy exposure. Analysis of the effects of control HU on plasma in the sham-irradiated animals showed that the alanine, aspartate, glutamate, riboflavin, and glutamine metabolisms as well as arginine biosynthesis were affected. The effects of control HU on the hippocampus in the sham-irradiated animals showed that the phenylalanine, tyrosine, and tryptophan pathway was affected the most. Analysis of effects of 0.75 Gy irradiation on the cortex of control HU animals showed that the glutamine and glutamate metabolic pathway was affected similar to the hippocampus, while the riboflavin pathway was affected in animals that were not under the control HU condition. The effects of control HU on the cortex in sham-irradiated animals showed that the riboflavin metabolic pathway was affected. Animals receiving 0.75 Gy of irradiation showed impaired glutamine and glutamate metabolic pathway, whereas animals receiving 1.5 Gy of irradiation showed impaired riboflavin metabolic pathways. A total of 21 plasma metabolites were correlated with the behavioral measures, indicating that plasma and brain biomarkers associated with behavioral performance are dependent on the environmental conditions experienced.DISCUSSION: Phenylalanine, tyrosine, and tryptophan metabolism as well as phenylalanine and tryptophan as plasma metabolites are biomarkers that can be considered for spaceflight as they were revealed in both Fischer and WAG/Rij rats exposed to simGCRsim and/or HU.PMID:39605860 | PMC:PMC11598337 | DOI:10.3389/fphys.2024.1486767

bioRxiv [Preprint]. 2024 Nov 15:2024.11.13.623458. doi: 10.1101/2024.11.13.623458.ABSTRACTDespite decades of study, large parts of the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands of small molecule-associated peaks within human tissues and biofluids, but typically only a small fraction of these can be identified, and structure elucidation of novel metabolites remains a low-throughput endeavor. Biochemical large language models have transformed the interpretation of DNA, RNA, and protein sequences, but have not yet had a comparable impact on understanding small molecule metabolism. Here, we present an approach that leverages chemical language models to discover previously uncharacterized metabolites. We introduce DeepMet, a chemical language model that learns the latent biosynthetic logic embedded within the structures of known metabolites and exploits this understanding to anticipate the existence of as-of-yet undiscovered metabolites. Prospective chemical synthesis of metabolites predicted to exist by DeepMet directs their targeted discovery. Integrating DeepMet with tandem mass spectrometry (MS/MS) data enables automated metabolite discovery within complex tissues. We harness DeepMet to discover several dozen structurally diverse mammalian metabolites. Our work demonstrates the potential for language models to accelerate the mapping of the metabolome.PMID:39605668 | PMC:PMC11601323 | DOI:10.1101/2024.11.13.623458

bioRxiv [Preprint]. 2024 Nov 15:2024.11.12.623208. doi: 10.1101/2024.11.12.623208.ABSTRACTSUMMARY: The integration of metabolomics with other omics ("multi-omics") offers complementary insights into disease biology. However, this integration remains challenging due to the fragmented landscape of current methodologies, which often require programming experience or bioinformatics expertise. Moreover, existing approaches are limited in their ability to accommodate unidentified metabolites, resulting in the exclusion of a significant portion of data from untargeted metabolomics experiments. Here, we introduce iModMix , a novel approach that uses a graphical lasso to construct network modules for integration and analysis of multi-omics data. iModMix uses a horizontal integration strategy, allowing metabolomics data to be analyzed alongside proteomics or transcriptomics to explore complex molecular associations within biological systems. Importantly, it can incorporate both annotated and unidentified metabolites, addressing a key limitation of existing methodologies. iModMix is available as a user-friendly R Shiny application that requires no programming experience ( https://imodmix.moffitt.org ), and it includes example data from several publicly available multi-omic studies for exploration. An R package is available for advanced users ( https://github.com/biodatalab/iModMix ).AVAILABILITY AND IMPLEMENTATION: Shiny application: https://imodmix.moffitt.org . The R package and source code: https://github.com/biodatalab/iModMix .PMID:39605665 | PMC:PMC11601443 | DOI:10.1101/2024.11.12.623208

bioRxiv [Preprint]. 2024 Nov 21:2024.11.20.622298. doi: 10.1101/2024.11.20.622298.ABSTRACTEmerging evidence suggests the microbiome critically influences the onset and progression of neurodegenerative diseases; however, the identity of neuroprotective bacteria and the molecular mechanisms that respond within the host remain largely unknown. We took advantage of Caenorhabditis elegans' well characterized nervous system and ability to eat uni-bacterial diets to determine how metabolites and neuroprotective molecules from single species of bacteria suppress degeneration of motor neurons. We found Comamonas aquatica significantly protects against degeneration induced by overexpressing a key regulator of axon degeneration, TIR-1/SARM1. Genetic analyses and metabolomics reveal Comamonas protects against neurodegeneration by providing sufficient Vitamin B12 to activate METR-1/MTR methionine synthase in the intestine, which then lowers toxic levels of homocysteine in TIR-1-expressing animals. Defining a molecular pathway between Comamonas and neurodegeneration adds significantly to our understanding of gut-brain interactions and, given the prominent role of homocysteine in neurodegenerative disorders, reveals how such a bacterium could protect against disease.PMID:39605655 | PMC:PMC11601612 | DOI:10.1101/2024.11.20.622298